Table 4 Correlation of mouse mammary stem-like gene expression and breast tumor prognosis signatures

Melk – protein phosphorylation

Gpr126 – neuropeptide signaling pathway

Tmeff1 – development

Diap3 – cytoskeleton organization

Akap2 – unknown function

Exoc7 – protein transport

Ext1 – ossification

Oxct1 – metabolic process

Slc2a3 – transmembrane transport

Ect2 – signaling cascade

Fbxo31 – ubiquitin-dependent protein catabolic process

Lpcat1 – metabolic process

Uchl5 – ubiquitin-dependent protein catabolic process

Igfbp5 – regulation of cell growth

Egln1 – oxygen homeostasis

DC13 – unknown function

Esm1 – regulation of cell growth

Pitrm1 – proteolysis

Gmps – purine base biosynthetic process

Cdc42bpa – protein phosphorylation

Dck – pyrimidine nucleotide metabolic process

Gpr180 – unknown function

Rcf4 – DNA replication

Mmp9 – regulation of apoptosis

Orc6l – DNA replication

Hrasls – regulation of cell growth

Dtl – DNA replication

Flt1 – regulation of cell proliferation

Cenpa – nucleosome assembly

Prc1 – cell cycle

Ccne2 – cell cycle

Kntc2 – cell cycle

Mcm6 – cell cycle

Nusap1 – cell cycle

Good prognosis: 12 genes, none of which (0%) changed in stem-like stage

0 genes

0 genes

12 genes

Ap2b1 – protein transport

Ms4a7 – signal transduction

Stk32b – protein phosphorylation

Scube2 – calcium ion binding

Aldh4a1 – proline catabolic process

Gstm3 – metabolic process

Peci – metabolic process

Ebf4 – regulation of transcription

Bbc3 – induction of apoptosis

Tgfb3 – cell growth/signal transduction

Fgf18 – regulation of cell proliferation

Wisp1 – regulation of cell growth